Biological systems are complex systems because they are made up of a large number of interacting heterogeneous components. While interacting, these components create a structural unity that may be, for instance, a cell, an organism or a species. The central objective of systems biology is to identify the mechanisms by which the interactions between a biological system's components lead to the emergence and maintenance of such a global structural unity. We propose here to use individual-based modeling in order to explore the behavior of complex biological systems and to produce new hypothesis.We present the models we have developed in the field of computational neurosciences, evolutionary biology and cell models. In these three fields, we present the scientific questions we address, the models we developed and the main results we obtained.